Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HNF4A

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived pancreatic cells
NA
NA

Attributes by original data submitter

Sample

source_name
ES-derived progenitors
differentiation stages
Early pancreatic progenitor
genotype
wild type
antibody
HNF4A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA. Samples were amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix. The concentration of samples was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced single end or paired, as specified, on Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
15412262
Reads aligned (%)
92.5
Duplicates removed (%)
1.4
Number of peaks
412 (qval < 1E-05)

hg19

Number of total reads
15412262
Reads aligned (%)
91.5
Duplicates removed (%)
1.6
Number of peaks
366 (qval < 1E-05)

Base call quality data from DBCLS SRA